Is RBP3 p.Ser26= (c.78C>T) pathogenic?

RBP3 p.Ser26= (c.78C>T) is classified Benign/Likely benign in RBP3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-26). Low-frequency (popmax 3.41%, afr); Associated with retinitis pigmentosa.

What condition is associated with RBP3 p.Ser26= (c.78C>T)?

RBP3 p.Ser26= (c.78C>T) is associated with retinitis pigmentosa (ClinVar).

How common is RBP3 p.Ser26= (c.78C>T) in the general population?

RBP3 p.Ser26= (c.78C>T) is low-frequency (popmax 3.41%, afr) (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

RBP3 p.Ser26=

c.78C>T · rs115562835 · VCV299997

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.41%, afr)

Conditions

retinitis pigmentosa

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.25	GERP -1.7, phastCons 0.13
Overall
CADD	7.048	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.41% African / African-American · 2,561/75,044 alleles

Filtering AF 3.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.26%

Overall 0.185% 2,980/1,612,848 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.41%	29
Admixed American	0.308%	324
Remaining individualsnot grpmax-eligible	0.258%	388
Middle Eastern	0.148%	674
Ashkenazi Jewishnot grpmax-eligible	0.0372%	2,692
South Asian	0.00439%	22,770
European (non-Finnish)	0.00415%	24,082

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: RBP3
Protein: p.Ser26=
Coding: c.78C>T
MANE Select: NM_005225 · reported on NM_002900
dbSNP: rs115562835
Type: single nucleotide variant
Location: chr10:47348562 (GRCh38)
Structure: AlphaFold pLDDT 63.40 · 8 PDB

Full RBP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinitis pigmentosa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

RBP3 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala312Thr Uncertain significance ★★ same condition
RBP3 p.Ala379Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala403Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala688Val Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala803Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Arg170Gln Uncertain significance ★★ ⚠ same condition
RBP3 p.Arg323Cys Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rbp3-p-ser26 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown